Merge pull request #274 from microsoft/dotliquid

Improve CCDA Template and small update for converter engine
microsoft · Jul 16, 2021 · 0a7363e · 0a7363e
2 parents a2460a7 + f968bf7
commit 0a7363e
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diff --git a/data/SampleData/Ccda/170.314B2_Amb_CCD.ccda b/data/SampleData/Ccda/170.314B2_Amb_CCD.ccda
@@ -1027,7 +1027,7 @@
 													<originalText>
 														<reference value="#ID0EBALACA"/>
 													</originalText>
-													<translation xsi:type="CD" code="2670" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT" displayName="Codeine"/>
+													<translation xsi:type="CD" code="261000" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT" displayName="Codeine phosphate"/>
 												</code>
 												<name>Codeine</name>
 											</playingEntity>

diff --git a/data/SampleData/Ccda/C-CDA_R2-1_CCD.xml.ccda b/data/SampleData/Ccda/C-CDA_R2-1_CCD.xml.ccda
@@ -692,7 +692,7 @@
 									<participant typeCode="CSM">
 										<participantRole classCode="MANU">
 											<playingEntity classCode="MMAT">
-												<code code="70618" displayName="Penicillin" codeSystem="2.16.840.1.113883.6.88" codeSystemName="RxNorm"/>
+												<code code="7980" displayName="Penicillin" codeSystem="2.16.840.1.113883.6.88" codeSystemName="RxNorm"/>
 											</playingEntity>
 										</participantRole>
 									</participant>
@@ -2626,7 +2626,7 @@
 							<statusCode code="completed"/>
 							<effectiveTime value="20120512"/>
 							<methodCode nullFlavor="UNK"/>
-							<targetSiteCode code="appropriate_code" displayName="colon" codeSystem="2.16.840.1.113883.3.88.12.3221.8.9" codeSystemName="Body Site Value Set"/>
+							<targetSiteCode code="485005" displayName="colon" codeSystem="2.16.840.1.113883.3.88.12.3221.8.9" codeSystemName="Body Site Value Set"/>
 							<specimen typeCode="SPC">
 								<specimenRole classCode="SPEC">
 									<id root="c2ee9ee9-ae31-4628-a919-fec1cbb58683"/>

diff --git a/data/SampleData/Ccda/Consultation_Note.ccda b/data/SampleData/Ccda/Consultation_Note.ccda
@@ -398,7 +398,7 @@ ALLERGIES AND INTOLERANCES SECTION (ENTRIES REQUIRED) V2
 									<participant typeCode="CSM">
 										<participantRole classCode="MANU">
 											<playingEntity classCode="MMAT">
-												<code code="70618" displayName="Penicillin" codeSystem="2.16.840.1.113883.6.88" codeSystemName="RxNorm"/>
+												<code code="7980" displayName="Penicillin" codeSystem="2.16.840.1.113883.6.88" codeSystemName="RxNorm"/>
 											</playingEntity>
 										</participantRole>
 									</participant>

diff --git a/data/SampleData/Ccda/Discharge_Summary.ccda b/data/SampleData/Ccda/Discharge_Summary.ccda
@@ -737,7 +737,7 @@
 				<section>
 					<templateId root="2.16.840.1.113883.10.20.22.2.24" extension="2014-06-09"/>
 					<id extension="9937012" root="2.16.840.1.113883.19"/>
-					<code code="C-CDAV2-DDN" displayName="Hospital Discharge Diagnosis" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC"/>
+					<code code="11535-2" displayName="Hospital Discharge Diagnosis" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC"/>
 					<title>DISCHARGE DIAGNOSIS</title>
 					<text>
 						<content ID="DschDx">Appendicitis</content>

diff --git a/data/SampleData/Ccda/Progress_Note.ccda b/data/SampleData/Ccda/Progress_Note.ccda
@@ -475,7 +475,7 @@ Allergies, Adverse Reactions, Alerts
 									<participant typeCode="CSM">
 										<participantRole classCode="MANU">
 											<playingEntity classCode="MMAT">
-												<code code="70618" displayName="Penicillin" codeSystem="2.16.840.1.113883.6.88" codeSystemName="RxNorm"/>
+												<code code="7980" displayName="Penicillin" codeSystem="2.16.840.1.113883.6.88" codeSystemName="RxNorm"/>
 											</playingEntity>
 										</participantRole>
 									</participant>

diff --git a/data/SampleData/Ccda/Referral_Note.ccda b/data/SampleData/Ccda/Referral_Note.ccda
@@ -27,7 +27,7 @@
 	<!-- DocumentID: unique ID for the document -->
 	<id root="6f1bd58b-c58f-40b7-b314-caf1294ed98b"/>
 	<!-- Referral Note -->
-	<code codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" code="57113-1" displayName="Referral Note"/>
+	<code codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" code="57133-1" displayName="Referral Note"/>
 	<!-- Use the name of the code as the title -->
 	<title>Referral Note</title>
 	<effectiveTime value="201309210500-0800"/>
@@ -560,7 +560,7 @@ ALLERGIES AND INTOLERANCES SECTION V2
 									<participant typeCode="CSM">
 										<participantRole classCode="MANU">
 											<playingEntity classCode="MMAT">
-												<code code="70618" displayName="Penicillin" codeSystem="2.16.840.1.113883.6.88" codeSystemName="RxNorm"/>
+												<code code="7980" displayName="Penicillin" codeSystem="2.16.840.1.113883.6.88" codeSystemName="RxNorm"/>
 											</playingEntity>
 										</participantRole>
 									</participant>

diff --git a/data/SampleData/Ccda/Transfer_Summary.ccda b/data/SampleData/Ccda/Transfer_Summary.ccda
@@ -532,7 +532,7 @@ ALLERGIES AND INTOLERANCES SECTION (ENTRIES REQUIRED) V2
                   <participant typeCode="CSM">
                     <participantRole classCode="MANU">
                       <playingEntity classCode="MMAT">
-                        <code code="70618" displayName="Penicillin" codeSystem="2.16.840.1.113883.6.88"
+                        <code code="7980" displayName="Penicillin" codeSystem="2.16.840.1.113883.6.88"
                           codeSystemName="RxNorm" />
                       </playingEntity>
                     </participantRole>
@@ -1321,7 +1321,7 @@ HOSPITAL DISCHARGE DIAGNOSIS SECTION V2
         <section>
           <!-- Discharge Summary Hospital Discharge Diagnosis Template Id -->
           <templateId root="2.16.840.1.113883.10.20.22.2.24" extension="2014-06-09" />
-          <code code="C-CDAV2-DDN" displayName="Discharge diagnosis narritive" codeSystem="2.16.840.1.113883.6.1"
+          <code code="11535-2" displayName="Discharge diagnosis narritive" codeSystem="2.16.840.1.113883.6.1"
             codeSystemName="LOINC" />
           <title>Hospital Discharge Diagnosis</title>
           <text>.Kidney Malrotation. Discharged August 1, 2013</text>

diff --git a/data/Templates/Ccda/Entry/HospitalDischargeMedication/_entry_act_entryRelationship.liquid b/data/Templates/Ccda/Entry/HospitalDischargeMedication/_entry_act_entryRelationship.liquid
@@ -2,8 +2,10 @@
 {% include 'Resource/MedicationAdministration' medicationAdministration: relationship.substanceAdministration, ID: substanceAdministrationId -%}
 {% assign manufacturedMaterialId = relationship.substanceAdministration.consumable.manufacturedProduct.manufacturedMaterial | to_json_string | generate_uuid -%}
 {% include 'Resource/Medication' medication: relationship.substanceAdministration.consumable.manufacturedProduct.manufacturedMaterial, ID: manufacturedMaterialId -%}
-{% assign organizationId = relationship.substanceAdministration.performer.assignedEntity.representedOrganization | to_json_string | generate_uuid -%}
-{% include 'Resource/Organization' organization: relationship.substanceAdministration.performer.assignedEntity.representedOrganization, ID: organizationId -%}
+{% if relationship.substanceAdministration.performer.assignedEntity.representedOrganization -%}
+    {% assign organizationId = relationship.substanceAdministration.performer.assignedEntity.representedOrganization | to_json_string | generate_uuid -%}
+    {% include 'Resource/Organization' organization: relationship.substanceAdministration.performer.assignedEntity.representedOrganization, ID: organizationId -%}
+{% endif -%}
 {% include 'Reference/MedicationAdministration/Subject' ID: substanceAdministrationId, REF: fullPatientId -%}
 {% assign fullManufacturedMaterialId = manufacturedMaterialId | prepend: 'Medication/' -%}
 {% include 'Reference/MedicationAdministration/MedicationReference' ID: substanceAdministrationId, REF: fullManufacturedMaterialId -%}

diff --git a/data/Templates/Ccda/Header.liquid b/data/Templates/Ccda/Header.liquid
@@ -12,13 +12,12 @@
     {% include 'Resource/Encounter' encounter: msg.ClinicalDocument.componentOf.encompassingEncounter ID: encounterId -%}
     {% assign fullEncounterId = encounterId | prepend: 'Encounter/' -%}
     {% include 'Reference/Composition/Encounter' ID: compositionId, REF: fullEncounterId -%}
-{% endif -%}
-
-{% if msg.ClinicalDocument.componentOf.encompassingEncounter.location -%}
-    {% assign locationId = msg.ClinicalDocument.componentOf.encompassingEncounter.location | to_json_string | generate_uuid -%}
-    {% include 'Resource/Location' location: msg.ClinicalDocument.componentOf.encompassingEncounter.location ID: locationId -%}
-    {% assign fullLocationId = locationId | prepend: 'Location/' -%}
-    {% include 'Reference/Encounter/Location_Location' ID: encounterId, REF: fullLocationId -%}
+    {% if msg.ClinicalDocument.componentOf.encompassingEncounter.location -%}
+        {% assign locationId = msg.ClinicalDocument.componentOf.encompassingEncounter.location | to_json_string | generate_uuid -%}
+        {% include 'Resource/Location' location: msg.ClinicalDocument.componentOf.encompassingEncounter.location ID: locationId -%}
+        {% assign fullLocationId = locationId | prepend: 'Location/' -%}
+        {% include 'Reference/Encounter/Location_Location' ID: encounterId, REF: fullLocationId -%}
+    {% endif -%}
 {% endif -%}
 
 {% if msg.ClinicalDocument.custodian.assignedCustodian.representedCustodianOrganization.name._ -%}
@@ -46,7 +45,7 @@
         {% endif -%}
     {% endif -%}
 
-    {% if author.assignedAuthor -%}
+    {% if author.assignedAuthor.assignedPerson -%}
         {% evaluate practitionerId using 'Utils/GenerateId' obj: author.assignedAuthor -%}
         {% include 'Resource/Practitioner' practitioner: author.assignedAuthor ID: practitionerId -%}
         {% assign fullPractitionerId = practitionerId | prepend: 'Practitioner/' -%}

diff --git a/data/Templates/Ccda/Resource/_AllergyIntolerance.liquid b/data/Templates/Ccda/Resource/_AllergyIntolerance.liquid
@@ -16,7 +16,7 @@
             [
                 {
                     "system": "http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical",
-                    "code":{% include 'ValueSet/AllergyStatus' code: allergyStatus.code -%},
+                    "code":"{{ allergyStatus.code | get_property: 'ValueSet/AllergyStatus' }}",
                 }
             ]
         },
@@ -31,7 +31,6 @@
                     "substance":{ {% include 'DataType/CodeableConcept' CodeableConcept: allergyEntry.participant.participantRole.playingEntity.code -%} },
                 {% endif -%}
 
-
                 {% if r.observation.templateId | to_json_string | contains: '"2.16.840.1.113883.10.20.22.4.9"' -%}
                     "manifestation":
                     [
@@ -43,14 +42,15 @@
                     ],
                     "onset": "{{ r.observation.effectiveTime.low.value | format_as_date_time }}", 
                 {% endif -%}
-
-                {% if r.observation.templateId | to_json_string | contains: '"2.16.840.1.113883.10.20.22.4.8"' -%}
-                    {% if r.observation.value.translation -%}
-                        "severity":{% include 'ValueSet/AllergySeverity' code: r.observation.value.translation.displayName -%},
-                    {% else -%}
-                        "severity":{% include 'ValueSet/AllergySeverity' code: r.observation.value.displayName -%},
+                {% for templateId in r.observation.templateId -%}
+                    {% if templateId.root == "2.16.840.1.113883.10.20.22.4.8" -%}
+                        {% if r.observation.value.translation -%}
+                            "severity":"{{ r.observation.value.translation.displayName | downcase | get_property: 'ValueSet/AllergySeverity' }}",
+                        {% else -%}
+                            "severity":"{{ r.observation.value.displayName | downcase | get_property: 'ValueSet/AllergySeverity' }}",
+                        {% endif -%}
                     {% endif -%}
-                {% endif -%}
+                {% endfor -%}
             },
             {% endfor -%}
 

diff --git a/data/Templates/Ccda/Resource/_Composition.liquid b/data/Templates/Ccda/Resource/_Composition.liquid
@@ -40,35 +40,37 @@
                 "period":
                 {
                     "start":"{{ composition.documentationOf.serviceEvent.effectiveTime.low.value | format_as_date_time }}",
+                    "end":"{{ composition.documentationOf.serviceEvent.effectiveTime.high.value | format_as_date_time }}",
                 },
             },
         ],
         "section":
         [
             {% assign components = composition.component.structuredBody.component | to_array -%}
             {% for component in components -%}
-            {
-                {% if component.section.title._ -%}
-                "title":"{{ component.section.title._ }}",
-                {% endif -%}
-                {% if component.section.title._ == null -%}
-                "title":"{{ component.section.code.displayName }}",
-                {% endif -%}
-                "text":
-                {
-                    "status":"generated",
+            {   
+                {% if component.section -%}
                     {% if component.section.title._ -%}
-                    "div":"<div xmlns=\"http://www.w3.org/1999/xhtml\">{{ component.section.title._ }}</div>",
+                    "title":"{{ component.section.title._ }}",
                     {% endif -%}
                     {% if component.section.title._ == null -%}
-                    "div":"<div xmlns=\"http://www.w3.org/1999/xhtml\">{{ component.section.code.displayName }}</div>",
+                    "title":"{{ component.section.code.displayName }}",
                     {% endif -%}
-                },
-                "code":
-                {
-                    {% include 'DataType/CodeableConcept' CodeableConcept: component.section.code -%}
-                },
-                "mode":"snapshot",
+                    "text":
+                    {
+                        "status":"generated",
+                        {% if component.section.title._ -%}
+                            "div":"<div xmlns=\"http://www.w3.org/1999/xhtml\">{{ component.section.title._ | escape }}</div>",
+                        {% else -%}
+                            "div":"<div xmlns=\"http://www.w3.org/1999/xhtml\">{{ component.section.code.displayName | escape }}</div>",
+                        {% endif -%}
+                    },
+                    "code":
+                    {
+                        {% include 'DataType/CodeableConcept' CodeableConcept: component.section.code -%}
+                    },
+                    "mode":"snapshot",
+                {% endif -%}
             },
             {% endfor -%}
         ],

diff --git a/data/Templates/Ccda/Resource/_Encounter.liquid b/data/Templates/Ccda/Resource/_Encounter.liquid
@@ -19,10 +19,6 @@
             {% include 'DataType/Coding' Coding: encounter.code -%}
             {% endif -%}
         },
-        "type":
-        [
-            { {% include 'DataType/CodeableConcept' CodeableConcept: encounter.code -%} },
-        ],
         "identifier":
         [
             {% assign ids = encounter.id | to_array -%}

diff --git a/data/Templates/Ccda/Resource/_Immunization.liquid b/data/Templates/Ccda/Resource/_Immunization.liquid
@@ -29,13 +29,17 @@
             {% assign manufacturedProducts = consumable.manufacturedProduct | to_array -%}
             {% for manufacturedProduct in manufacturedProducts -%}
                 {% if manufacturedProduct.templateId | to_json_string | contains '"2.16.840.1.113883.10.20.22.4.54"' -%}
-                    "vaccineCode":{ {% include 'DataType/CodeableConcept' CodeableConcept: manufacturedProduct.manufacturedMaterial.code -%} },
+                    {% if manufacturedProduct.manufacturedMaterial.code.translation -%}
+                        "vaccineCode":{ {% include 'DataType/CodeableConcept' CodeableConcept: manufacturedProduct.manufacturedMaterial.code.translation -%} },
+                    {% else -%}
+                        "vaccineCode":{ {% include 'DataType/CodeableConcept' CodeableConcept: manufacturedProduct.manufacturedMaterial.code -%} },
+                    {% endif -%}
                     "lotNumber":"{{ manufacturedProduct.manufacturedMaterial.IotNumberText._ }}",
                 {% endif -%}
             {% endfor -%}
         {% endfor -%}
 
-        "status":"{{immunization.statusCode.code}}",
+        "status":"{{immunization.statusCode.code | get_property: 'ValueSet/ImmunizationStatus' }}",
         "route":{ {% include 'DataType/CodeableConcept' CodeableConcept: immunization.routeCode -%}},
         "site":{ {% include 'DataType/CodeableConcept' CodeableConcept: immunization.approachSiteCode -%} },      
     },

diff --git a/data/Templates/Ccda/Resource/_MedicationAdministration.liquid b/data/Templates/Ccda/Resource/_MedicationAdministration.liquid
@@ -10,11 +10,12 @@
             { {% include 'DataType/Identifier' Identifier: id -%} },
             {% endfor -%}
         ],
-        "status":"{{ medicationAdministration.statusCode.code }}",
+        "status":"{{ medicationAdministration.statusCode.code | get_property: 'ValueSet/MedicationAdministrationStatus' }}",
         "effectivePeriod":
         {
-            "start":"{{ medicationAdministration.effectiveTime.low.value | format_as_date_time }}",
-            "end":"{{ medicationAdministration.effectiveTime.high.value | format_as_date_time }}",
+            {% assign effectiveTimes = medicationAdministration.effectiveTime | to_array -%}
+            "start":"{{ effectiveTimes.first.low.value | format_as_date_time }}",
+            "end":"{{ effectiveTimes.first.high.value | format_as_date_time }}",
         },
         "dosage":
         {

diff --git a/data/Templates/Ccda/Resource/_Patient.liquid b/data/Templates/Ccda/Resource/_Patient.liquid
@@ -25,7 +25,7 @@
             {% endfor -%}
         ],
         "birthDate":"{{ patientRole.patient.birthTime.value | add_hyphens_date }}",
-        "gender":"{{ patientRole.patient.administrativeGenderCode.displayName | downcase }}",
+        "gender":"{{ patientRole.patient.administrativeGenderCode.code | get_property: 'ValueSet/Gender' }}",
         "extension":
         [
             { {% include 'Extension/Race' Race: patientRole.patient -%} },
@@ -56,8 +56,8 @@
                     [
                         {
                             "system":"urn:ietf:bcp:47",
-                            "code":"{{ languageCommunication.languageCode.code }}",
-                            "display":"{{ languageCommunication.languageCode.code | downcase | get_property: 'ValueSet/Language' }}",
+                            "code":"{{ languageCommunication.languageCode.code | downcase | get_property: 'ValueSet/Language', , 'code'  }}",
+                            "display":"{{ languageCommunication.languageCode.code | downcase | get_property: 'ValueSet/Language', , 'display'  }}",
                         },
                     ],
                 },

diff --git a/data/Templates/Ccda/Resource/_Procedure.liquid b/data/Templates/Ccda/Resource/_Procedure.liquid
@@ -17,14 +17,17 @@
         "status":"{{ procedureEntry.statusCode.code }}",
         "code":
         {
-            {% if procedureEntry.code.translation -%}
-            {% include 'DataType/CodeableConcept' CodeableConcept: procedureEntry.code.translation -%}
-            {% endif -%}
-            {% if procedureEntry.code.translation == null -%}
             {% include 'DataType/CodeableConcept' CodeableConcept: procedureEntry.code -%}
-            {% endif -%}
         },
-        "performedDateTime":"{{ procedureEntry.effectiveTime.value | format_as_date_time }}",
+        {% if procedureEntry.effectiveTime.value -%}
+            "performedDateTime":"{{ procedureEntry.effectiveTime.value | format_as_date_time }}",
+        {% else -%}
+            "performedPeriod": 
+            {
+                "start":"{{ procedureEntry.effectiveTime.low.value | format_as_date_time }}",
+                "end":"{{ procedureEntry.effectiveTime.high.value | format_as_date_time }}",
+            },
+        {% endif -%}
         "bodySite":
         [
             { {% include 'DataType/CodeableConcept' CodeableConcept: procedureEntry.targetSiteCode -%} },

diff --git a/data/Templates/Ccda/Resource/_ServiceRequest.liquid b/data/Templates/Ccda/Resource/_ServiceRequest.liquid
@@ -20,8 +20,8 @@
             {% include 'DataType/CodeableConcept' CodeableConcept: serviceEntry.code -%}
             {% endif -%}
         },
-        "priority":"{{ serviceEntry.priorityCode.displayName }}",
-        "occuranceDateTime":"{{serviceEntry.effectiveTime.value | format_as_date_time }}",
+        "priority":"{{ serviceEntry.priorityCode.code  | get_property: 'ValueSet/ServiceRequestPriority' }}",
+        "occurrenceDateTime":"{{serviceEntry.effectiveTime.value | format_as_date_time }}",
     },
     "request":{
         "method":"PUT",

diff --git a/data/Templates/Ccda/Section/_HospitalAdmissionDiagnosis.liquid b/data/Templates/Ccda/Section/_HospitalAdmissionDiagnosis.liquid
@@ -1,2 +1,2 @@
 {% assign firstSections = msg | get_first_ccda_sections_by_template_id: '2.16.840.1.113883.10.20.22.4.34' -%}
-{{ firstSections.2_16_840_1_113883_10_20_22_4_34.entry | to_array | batch_render: 'Entry/_HospitalAdmissionDiagnosis/entry', 'entry' }}
+{{ firstSections.2_16_840_1_113883_10_20_22_4_34.entry | to_array | batch_render: 'Entry/HospitalAdmissionDiagnosis/entry', 'entry' }}